Pleasanton-based grocery giant Safeway has agreed to pay $600,000 to settle charges that the company is violating the federal Clean Air Act. Officials with the U.S. Environmental Protection Agency announced Wednesday that the supermarket chain will significantly reduce emissions from its refrigeration equipment — emissions that deplete the ozone layer.

The government says Safeway violated the nation’s clean air laws by not promptly fixing leaks of HCFC-22 — a heat-trapping gas that contributes to climate change — from its refrigerators. The government says Safeway also failed to keep proper maintenance records.

Safeway also agreed to reduce its companywide average leak rate from 25 percent to 18 percent or below by 2015.

To do so, it will invest an estimated $4.1 million in new systems, equipment upgrades and other changes meant to reduce leakage of the harmful gas.

EPA estimates the changes could prevent the future release of more than 100,000 pounds of the ozone-depleting refrigerants.

“Today’s settlement … will also achieve important climate benefits because these ozone-depleting substances are over 1,800 times more potent than carbon dioxide,” Jared Blumenfeld, EPA’s Pacific Southwest regional administrator, said.

Safeway said in a statement that environmental stewardship is important to the company and that it does not admit any liability for the alleged violations. The statement said the allegations date back prior to 2007, and don’t reflect improvements Safeway has made since then.

Safeway also operates Vons stores in Southern California and Nevada, Randalls in Texas and Carrs in Alaska.